I have now optimised my multiplex PCR, and am ready to start using my study cohort. This will be nearly 2000 reactions, which is a little overwhelming!

I have severe rheumatoid arthritis, mainly affecting my wrists and hands. It makes pipetting rather uncomfortable. I have tried electronic pipettes, but the extra weight is worse than using a manual. (Unfortunately, a robot is not an option!) I am considering using either a stepper pipette to plate my master mix, or a multichannel. A multichannel would significantly decrease the pipetting action, but I'm worried about finding a suitable reservoir as obviously the cost of the reagents prohibits making up lots of master mix to adequately fill a reservoir to easily use a multichannel pipette. The alternative would be to use the stepper, which would still require 96 "pipettes" per plate, but wouldn't require an aspiration pipette each time, or an excess volume of master mix. I am leaning towards the stepper, but I wondered whether anyone had any suggestions regarding reagent reservoirs for PCR that would make that option feasible?

One more very basic question... does adding sample to master mix rather than master mix to sample make a difference??

you can prepare PCR-strips (8 wells attached to each other) filled up with PCR mastermix as your reservoir (or individual PCR tubes). You just have to put them in an appropriate rack. Then you can use a multichannel pipette. The stepper is a bit difficult as sometime the speed is too high so that the mastermix goes everywhere but not in the tube.